Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Re: [Freesurfer] freesurfer
by Jenni Pacheco 16 Sep '08

16 Sep '08

Hi HweeLing, I think something like: mri_vol2vol -mov <input> -targ <template> -o <output> -interp nearest should work. As Doug says, you should use the aparc+aseg.mgz as your input. Use your MNI template as your target, and call your output whatever you want. Be sure to use the nearest neighbor interpolation method. This will put your whole aparc+aseg into MNI space, and then the label for STS is 1030 and 2030. Hope that works. Jenni On Tue, Sep 16, 2008 at 9:05 AM, Hwee Ling Lee < hwee-ling.lee(a)tuebingen.mpg.de> wrote: > Hi, > > I'm re-posting a question. > > Pardon my ignorance. > > How do I use this mri_vol2vol command? I tried to follow the notes, > however, > I'm not quite sure, hence I was not able to write a ROI mask. > > Cheers, > HL > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: 12 September 2008 18:10 > To: Bruce Fischl > Cc: freesurfer(a)nmr.mgh.harvard.edu; Hwee Ling Lee > Subject: Re: [Freesurfer] freesurfer > > You can also skip the 1st two steps and just convert aparc+aseg.mgz to > MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then > look for voxels with values 1030 (left STG) or 2030 (right STG). > > doug > > Bruce Fischl wrote: > > > Hi HweeLing, > > > > I think the aparc.a2005s has the STS labeled in it, so you should > > already have what you need in individual space. You could use > > mri_annot2label, mri_label2vol and mri_vol2vol to transform this into > > MNI if you need to. > > > > cheers, > > Bruce > > > > > > > > On Fri, 12 Sep 2008, Hwee Ling Lee wrote: > > > >> > >> Hi All, > >> > >> I was looking for methods to create a superior temporal sulcus > >> mask (upper and lower boundary). > >> > >>> From my understanding, Freesurfer does a pretty good job in labeling > >>> the > >> > >> sulcus, hence I was wondering if there are possible ways to write the > >> particular ROI as a mask image for each individual subject, and > >> preferably > >> to be in the MNI space or if not, at least in the native space. > >> > >> Thank you. > >> > >> Best wishes, > >> HweeLing > >> > >> > >> > >> ----------------------------------------------------------------------- > >> Hwee Ling, Lee > >> Max-Planck Institute for Biological Cybernetics > >> Cognitive Neuroimaging > >> Spemannstrasse 41 > >> 72076 Tuebingen > >> Germany > >> Tel: +49-70701-601-1785 > >> Fax: +49-7071-601-616 > >> hwee-ling.lee(a)tuebingen.mpg.de > >> hweeling.lee(a)gmail.com > >> http://www.kyb.mpg.de/~hweeling > >> ----------------------------------------------------------------------- > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: jpacheco(a)mail.utexas.edu

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Re: [Freesurfer] freesurfer
by Bruce Fischl 16 Sep '08

16 Sep '08

Hi HweeLing, I think the aparc.a2005s has the STS labeled in it, so you should already have what you need in individual space. You could use mri_annot2label, mri_label2vol and mri_vol2vol to transform this into MNI if you need to. cheers, Bruce On Fri, 12 Sep 2008, Hwee Ling Lee wrote: > > Hi All, > > I was looking for methods to create a superior temporal sulcus > mask (upper and lower boundary). >> From my understanding, Freesurfer does a pretty good job in labeling the > sulcus, hence I was wondering if there are possible ways to write the > particular ROI as a mask image for each individual subject, and preferably > to be in the MNI space or if not, at least in the native space. > > Thank you. > > Best wishes, > HweeLing > > > > ----------------------------------------------------------------------- > Hwee Ling, Lee > Max-Planck Institute for Biological Cybernetics > Cognitive Neuroimaging > Spemannstrasse 41 > 72076 Tuebingen > Germany > Tel: +49-70701-601-1785 > Fax: +49-7071-601-616 > hwee-ling.lee(a)tuebingen.mpg.de > hweeling.lee(a)gmail.com > http://www.kyb.mpg.de/~hweeling > ----------------------------------------------------------------------- > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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automation of tkmedit
by Jared Price 15 Sep '08

15 Sep '08

Hi everybody. This is Jared over at BWH. We are currently working on some manual editing of segmentation volumes. This requires repetitively switching the view between the segmentation volume and the black and white MRI volume as you edit. This is normally done in TkMedit with the control-g keystroke which activates the "Segmentation Overlay" command in the View menu. In editing the segmentation volume for any given patient the number of times that this keystroke is used is on the order of hundreds to thousands. What we would like to do is find a way to automate that keystroke so that during editing the view would automatically switch every 5 seconds or so between the black and white MRI image and the segmentation overlay. We use MAC OS X, leopard, and have thought of using automator or apple script to automate the command. We think this might be difficult to do because the "segmentation overlay" command cannot be elicited from Terminal (Terminal is Mac OS's command-line interface). If the "segmentation overlay" command could be elicited from a command-line prompt it should be a simple matter to create a script that would repetitively enter this command. Does anyone know how we could accomplish automation of this task within TkMedit? All the best, Jared Jared Price Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 1249 Boylston Street Boston, MA 02115 617-525-6076 jcp44(a)bwh.harvard.edu The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance Help Line at 800-856-1983 and properly dispose of this information.

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(no subject)
by Wang, Xin 15 Sep '08

15 Sep '08

Hello, Group, I have a hard time to register the functional ROIs to the exact location (x,y,z) on thickness map. I can't find articles that register the fsl result onto freesurfer thickness map and then do the ROI analysis. Could someone kindly list some references for me? I appreciate if anyone is willing to share his/her experience on registration of functional and thickness maps (especially ROIs). Thanks in advance, Xin

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Details on mysterious Longitudinal bug?
by Laluz, Victor 15 Sep '08

15 Sep '08

Hello, Can anyone give me some details on the longitudinal bug that Norbert Schuff discovered in Freesurfer, specifically, what it is, if there is any way to avoid it, and what versions it applies to. We have already sent an email to Norbert Schuff directly, but maybe someone else knows more about it? Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax)

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Re: [Freesurfer] Errors on the Linux86_64 GNU machine
by Nick Schmansky 15 Sep '08

15 Sep '08

HweeLing, This line: Linux zeus.AC.kyb.local 2.6.18-53.1.4.el5 #1 SMP Fri Nov 30 00:45:16 EST 2007 i686 i686 i386 GNU/Linux indicates that your OS is 32bit. try the freesurfer centos4 install, or, alternatively, if you're sure you have a 64bit machine (see uname - m), then boot the 64bit OS. Nick On Mon, 2008-09-15 at 16:05 +0200, Hwee Ling Lee wrote: > Hi, > > > > I tried to convert DICOM images into freesurfer compatible images > using a linux machine. > > However, I get this error message: > > [hweeling@zeus hweeling]$ recon-all - > i /home/raid/hweeling/DICOM/AVE02_S15.MR.MPI_STANDARD_USERS.8.2.2008.04.08.11.29.54.171875.29050922.IMA -s S15_fs > > INFO: SUBJECTS_DIR is /home/raid/hweeling/freesurfer/subjects > > Actual FREESURFER_HOME /home/raid/hweeling/freesurfer > > Linux zeus.AC.kyb.local 2.6.18-53.1.4.el5 #1 SMP Fri Nov 30 00:45:16 > EST 2007 i686 i686 i386 GNU/Linux > > /home/raid/hweeling/freesurfer//bin/mri_convert: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/flirt: Exec format error. Binary > file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_convert: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/tkregister2_cmdl: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_normalize: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_watershed: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_segment: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_label2label: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_em_register: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_ca_normalize: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_ca_register: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_ca_label: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_pretess: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_fill: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_tessellate: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_concatenate_lta: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mri_normalize_tp2: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_smooth: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_inflate: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_curvature: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_sphere: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_fix_topology: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_topo_fixer: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_ca_label: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_euler_number: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_make_surfaces: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_register: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mris_anatomical_stats: Exec format > error. Binary file not executable. > > /home/raid/hweeling/freesurfer//bin/mrisp_paint: Exec format error. > Binary file not executable. > > /home/raid/hweeling/freesurfer/subjects/S15_fs > > > > mri_convert /home/raid/hweeling/DICOM/AVE02_S15.MR.MPI_STANDARD_USERS.8.2.2008.04.08.11.29.54.171875.29050922.IMA /home/raid/hweeling/freesurfer/subjects/S15_fs/mri/orig/001.mgz > > > > /home/raid/hweeling/freesurfer//bin/mri_convert: Exec format error. > Binary file not executable. > > Linux zeus.AC.kyb.local 2.6.18-53.1.4.el5 #1 SMP Fri Nov 30 00:45:16 > EST 2007 i686 i686 i386 GNU/Linux > > > > recon-all exited with ERRORS at Mon Sep 15 16:02:31 CEST 2008 > > > > > > what might have gone wrong? > > > > Cheers, > > HweeLing > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Errors on the Linux86_64 GNU machine
by Hwee Ling Lee 15 Sep '08

15 Sep '08

Hi, I tried to convert DICOM images into freesurfer compatible images using a linux machine. However, I get this error message: [hweeling@zeus hweeling]$ recon-all -i /home/raid/hweeling/DICOM/AVE02_S15.MR.MPI_STANDARD_USERS.8.2.2008.04.08.11. 29.54.171875.29050922.IMA -s S15_fs INFO: SUBJECTS_DIR is /home/raid/hweeling/freesurfer/subjects Actual FREESURFER_HOME /home/raid/hweeling/freesurfer Linux zeus.AC.kyb.local 2.6.18-53.1.4.el5 #1 SMP Fri Nov 30 00:45:16 EST 2007 i686 i686 i386 GNU/Linux /home/raid/hweeling/freesurfer//bin/mri_convert: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/flirt: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_convert: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/tkregister2_cmdl: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_normalize: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_watershed: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_segment: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_label2label: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_em_register: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_ca_normalize: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_ca_register: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_ca_label: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_pretess: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_fill: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_tessellate: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_concatenate_lta: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mri_normalize_tp2: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_smooth: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_inflate: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_curvature: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_sphere: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_fix_topology: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_topo_fixer: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_ca_label: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_euler_number: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_make_surfaces: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_register: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mris_anatomical_stats: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer//bin/mrisp_paint: Exec format error. Binary file not executable. /home/raid/hweeling/freesurfer/subjects/S15_fs mri_convert /home/raid/hweeling/DICOM/AVE02_S15.MR.MPI_STANDARD_USERS.8.2.2008.04.08.11. 29.54.171875.29050922.IMA /home/raid/hweeling/freesurfer/subjects/S15_fs/mri/orig/001.mgz /home/raid/hweeling/freesurfer//bin/mri_convert: Exec format error. Binary file not executable. Linux zeus.AC.kyb.local 2.6.18-53.1.4.el5 #1 SMP Fri Nov 30 00:45:16 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Sep 15 16:02:31 CEST 2008 what might have gone wrong? Cheers, HweeLing

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mris_volmask error
by Dahlia Sharon 12 Sep '08

12 Sep '08

Hi, I ran recon-all, and it exited with an error at this command: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance subj10 The error message reads: mris_volmask.bin: error while loading shared libraries: libvtkpng.so.5.2: cannot open shared object file: No such file or directory On the off-chance that it's missing an input file, I made sure that I have orig.mgz in the mri folder and ?h.white and pial in the surf folder. Does anyone have an idea what could be wrong here? Thanks! Dahlia.

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tksurfer woes
by Hoptman, Matthew 12 Sep '08

12 Sep '08

Hi all, I'm having trouble using freesurfer's tksurfer program (I only get a sliver of the brain). Here is the error info I get: [ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects surfer: Reading header info from /home/freesurfer/subjects/77059/mri/T1.mgz surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName "ES1000 515E" BusID "14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes" Section "DRI" Group "video" Mode 0660 EndSection I'm have an onboard ATI ES1000 515E graphics chip. Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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ces and percent signal change
by Reza Rajimehr 12 Sep '08

12 Sep '08

Hi, For a stimulus condition 'A' and a fixation condition, does the ces file for the contrast 'A - fix' correspond to the % signal change for the condition A? Thanks, Reza ************************************ Reza Rajimehr, MD Postdoctoral Research Fellow NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th Street Charlestown, MA 02129 Phone: 617-669-0930 Email: reza(a)nmr.mgh.harvard.edu ************************************

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Freesurfer